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Iron in PDB 4yrw: Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant

Enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant

All present enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, PDB code: 4yrw was solved by K.Okamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.33 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.497, 138.468, 222.213, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.9

Other elements in 4yrw:

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant (pdb code 4yrw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, PDB code: 4yrw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4yrw

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Iron binding site 1 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:24.0
occ:1.00
 FE1 A:FES3001 0.0 24.0 1.0
S2 A:FES3001 2.2 25.9 1.0
SG A:CYS112 2.2 22.1 1.0
S1 A:FES3001 2.3 29.8 1.0
FE2 A:FES3001 2.7 23.4 1.0
SG A:CYS149 3.0 31.5 1.0
CB A:CYS112 3.2 22.8 1.0
O A:HOH3331 3.5 21.2 1.0
CB A:CYS149 3.5 21.1 1.0
N A:CYS112 3.6 22.0 1.0
CA A:CYS112 3.8 21.4 1.0
N A:GLY113 3.9 17.2 1.0
N A:CYS149 4.2 20.7 1.0
C A:CYS112 4.2 18.4 1.0
N A:PHE114 4.4 19.1 1.0
SG A:CYS147 4.4 25.2 1.0
CA A:CYS149 4.5 22.9 1.0
SG A:CYS115 4.5 25.7 1.0
C A:GLN111 4.7 24.0 1.0
N A:ARG148 4.8 22.4 1.0
N A:CYS115 4.9 16.8 1.0
CA A:GLY113 5.0 18.5 1.0
CB A:GLN111 5.0 22.3 1.0

Iron binding site 2 out of 8 in 4yrw

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Iron binding site 2 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:23.4
occ:1.00
 FE2 A:FES3001 0.0 23.4 1.0
SG A:CYS115 2.2 25.7 1.0
S1 A:FES3001 2.2 29.8 1.0
S2 A:FES3001 2.2 25.9 1.0
SG A:CYS147 2.3 25.2 1.0
FE1 A:FES3001 2.7 24.0 1.0
CB A:CYS147 3.2 24.1 1.0
CB A:CYS115 3.4 21.0 1.0
CA A:CYS147 3.7 21.6 1.0
N A:ARG148 4.1 22.4 1.0
N A:CYS115 4.2 16.8 1.0
C A:CYS147 4.3 22.6 1.0
N A:CYS149 4.3 20.7 1.0
O A:HOH3128 4.4 22.0 1.0
CA A:CYS115 4.4 17.9 1.0
CB A:CYS149 4.5 21.1 1.0
SG A:CYS112 4.7 22.1 1.0
CG2 A:THR150 4.8 24.4 1.0
O A:LEU146 4.9 23.1 1.0
SG A:CYS149 4.9 31.5 1.0
N A:CYS147 5.0 21.4 1.0

Iron binding site 3 out of 8 in 4yrw

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Iron binding site 3 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:19.6
occ:1.00
 FE1 A:FES3002 0.0 19.6 1.0
S1 A:FES3002 2.2 25.5 1.0
S2 A:FES3002 2.2 24.6 1.0
SG A:CYS51 2.3 20.2 1.0
SG A:CYS73 2.3 22.5 1.0
FE2 A:FES3002 2.8 21.5 1.0
CB A:CYS73 3.2 23.3 1.0
CB A:CYS51 3.4 20.1 1.0
ND2 A:ASN71 4.2 26.9 1.0
N A:CYS73 4.3 19.6 1.0
CB A:ASN71 4.3 26.0 1.0
N A:GLY46 4.3 24.0 1.0
N A:CYS51 4.3 18.8 1.0
CA A:CYS73 4.3 22.0 1.0
N A:GLY44 4.3 24.5 1.0
SG A:CYS43 4.4 25.3 1.0
CA A:CYS51 4.5 19.3 1.0
CA A:GLY46 4.6 24.0 1.0
CG A:ASN71 4.6 29.6 1.0
CA A:GLY44 4.7 21.8 1.0
SG A:CYS48 4.7 21.5 1.0
N A:GLU45 4.8 24.5 1.0
N A:GLY49 4.9 18.5 1.0
CA A:ASN71 5.0 25.3 1.0
C A:GLY44 5.0 23.9 1.0

Iron binding site 4 out of 8 in 4yrw

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Iron binding site 4 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:21.5
occ:1.00
 FE2 A:FES3002 0.0 21.5 1.0
S2 A:FES3002 2.2 24.6 1.0
S1 A:FES3002 2.3 25.5 1.0
SG A:CYS48 2.3 21.5 1.0
SG A:CYS43 2.4 25.3 1.0
FE1 A:FES3002 2.8 19.6 1.0
N A:CYS43 3.4 23.9 1.0
CB A:CYS43 3.5 22.5 1.0
CB A:CYS48 3.5 21.5 1.0
N A:CYS48 3.5 21.4 1.0
N A:GLY44 3.8 24.5 1.0
CA A:CYS43 3.8 23.9 1.0
N A:GLY49 3.8 18.5 1.0
CA A:CYS48 3.9 19.5 1.0
C A:GLY42 4.1 23.3 1.0
C A:CYS43 4.2 23.5 1.0
C A:CYS48 4.2 20.5 1.0
N A:GLY42 4.4 24.2 1.0
N A:ALA50 4.4 19.4 1.0
N A:GLY46 4.5 24.0 1.0
N A:GLY47 4.5 23.1 1.0
CA A:GLY42 4.5 22.8 1.0
SG A:CYS73 4.6 22.5 1.0
SG A:CYS51 4.6 20.2 1.0
N A:GLU45 4.7 24.5 1.0
C A:GLY47 4.7 25.2 1.0
CA A:GLY49 4.8 20.2 1.0
CA A:GLY44 4.8 21.8 1.0
C A:GLY46 4.9 22.5 1.0
CA A:GLY46 4.9 24.0 1.0
O A:GLY42 4.9 25.1 1.0

Iron binding site 5 out of 8 in 4yrw

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Iron binding site 5 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:22.2
occ:1.00
 FE1 B:FES4001 0.0 22.2 1.0
S2 B:FES4001 2.2 25.1 1.0
SG B:CYS112 2.3 20.1 1.0
S1 B:FES4001 2.3 25.8 1.0
FE2 B:FES4001 2.7 20.6 1.0
SG B:CYS149 2.8 30.2 1.0
CB B:CYS112 3.3 19.5 1.0
CB B:CYS149 3.5 22.7 1.0
N B:CYS112 3.5 18.2 1.0
O B:HOH4415 3.6 17.1 1.0
CA B:CYS112 3.9 18.9 1.0
N B:GLY113 3.9 18.6 1.0
N B:CYS149 4.2 19.8 1.0
C B:CYS112 4.3 18.8 1.0
N B:PHE114 4.4 17.5 1.0
SG B:CYS147 4.4 22.8 1.0
CA B:CYS149 4.5 21.5 1.0
SG B:CYS115 4.6 22.2 1.0
C B:GLN111 4.7 20.1 1.0
N B:ARG148 4.8 20.8 1.0
CB B:GLN111 4.9 21.7 1.0
N B:CYS115 5.0 17.6 1.0

Iron binding site 6 out of 8 in 4yrw

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Iron binding site 6 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:20.6
occ:1.00
 FE2 B:FES4001 0.0 20.6 1.0
S1 B:FES4001 2.2 25.8 1.0
SG B:CYS115 2.2 22.2 1.0
S2 B:FES4001 2.2 25.1 1.0
SG B:CYS147 2.4 22.8 1.0
FE1 B:FES4001 2.7 22.2 1.0
CB B:CYS147 3.3 22.6 1.0
CB B:CYS115 3.4 18.0 1.0
CA B:CYS147 3.8 19.2 1.0
N B:ARG148 4.2 20.8 1.0
N B:CYS115 4.3 17.6 1.0
O B:HOH4107 4.3 18.1 1.0
C B:CYS147 4.4 18.2 1.0
CA B:CYS115 4.4 16.0 1.0
N B:CYS149 4.4 19.8 1.0
CB B:CYS149 4.5 22.7 1.0
CG2 B:THR150 4.6 24.5 1.0
SG B:CYS112 4.7 20.1 1.0
SG B:CYS149 4.9 30.2 1.0
O B:LEU146 5.0 20.6 1.0

Iron binding site 7 out of 8 in 4yrw

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Iron binding site 7 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:15.1
occ:1.00
 FE1 B:FES4002 0.0 15.1 1.0
S1 B:FES4002 2.2 18.9 1.0
S2 B:FES4002 2.2 18.2 1.0
SG B:CYS51 2.3 19.0 1.0
SG B:CYS73 2.3 18.1 1.0
FE2 B:FES4002 2.8 16.0 1.0
CB B:CYS73 3.1 17.2 1.0
CB B:CYS51 3.5 16.2 1.0
N B:CYS73 4.2 19.0 1.0
CB B:ASN71 4.2 14.8 1.0
N B:GLY46 4.3 21.8 1.0
CA B:CYS73 4.3 18.9 1.0
ND2 B:ASN71 4.3 17.4 1.0
N B:CYS51 4.3 15.5 1.0
SG B:CYS43 4.4 19.3 1.0
N B:GLY44 4.4 19.8 1.0
CA B:GLY46 4.5 23.0 1.0
CA B:CYS51 4.5 16.4 1.0
CG B:ASN71 4.5 17.6 1.0
CA B:GLY44 4.7 19.3 1.0
SG B:CYS48 4.7 18.4 1.0
N B:GLU45 4.7 21.3 1.0
CA B:ASN71 4.9 16.1 1.0
N B:GLY49 4.9 15.9 1.0
C B:GLY44 4.9 21.7 1.0

Iron binding site 8 out of 8 in 4yrw

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Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:16.0
occ:1.00
 FE2 B:FES4002 0.0 16.0 1.0
S2 B:FES4002 2.3 18.2 1.0
S1 B:FES4002 2.3 18.9 1.0
SG B:CYS48 2.3 18.4 1.0
SG B:CYS43 2.3 19.3 1.0
FE1 B:FES4002 2.8 15.1 1.0
N B:CYS43 3.4 17.9 1.0
CB B:CYS43 3.4 18.5 1.0
CB B:CYS48 3.5 17.4 1.0
N B:CYS48 3.6 18.6 1.0
N B:GLY44 3.8 19.8 1.0
CA B:CYS43 3.9 17.7 1.0
CA B:CYS48 3.9 17.8 1.0
N B:GLY49 3.9 15.9 1.0
C B:GLY42 4.1 18.0 1.0
C B:CYS48 4.2 18.7 1.0
C B:CYS43 4.2 18.1 1.0
N B:GLY42 4.3 16.1 1.0
CA B:GLY42 4.3 18.1 1.0
N B:GLY46 4.4 21.8 1.0
N B:ALA50 4.5 15.7 1.0
SG B:CYS73 4.5 18.1 1.0
N B:GLU45 4.6 21.3 1.0
N B:GLY47 4.6 21.3 1.0
SG B:CYS51 4.6 19.0 1.0
C B:GLY47 4.7 24.3 1.0
CA B:GLY46 4.8 23.0 1.0
C B:GLY46 4.8 26.6 1.0
CA B:GLY49 4.8 16.6 1.0
CA B:GLY44 4.9 19.3 1.0
O B:GLY42 4.9 16.3 1.0

Reference:

T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino. The C-Terminal Peptide Plays A Role in the Formation of An Intermediate Form During the Transition Between Xanthine Dehydrogenase and Xanthine Oxidase Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25817260
DOI: 10.1111/FEBS.13277
Page generated: Mon Aug 5 16:40:02 2024

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